From b6834ea0c46ee2eff0a28696de1c13ab5ecfd7dc Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 22 Dec 2023 11:27:27 -0800
Subject: [PATCH 1/2] Add nextclade3 via direct download

Nextclade v3 is not yet released in Bioconda. Add it as a direct
download so that users of Nextstrain's Conda runtime can transition to
using nextclade3.
---
 src/build.sh      |  6 ++++++
 src/target-triple | 23 +++++++++++++++++++++++
 2 files changed, 29 insertions(+)
 create mode 100755 src/target-triple

diff --git a/src/build.sh b/src/build.sh
index 67801e6..e87e1eb 100644
--- a/src/build.sh
+++ b/src/build.sh
@@ -1,4 +1,10 @@
 #!/usr/bin/env bash
 set -euo pipefail -x
 mkdir -p "$PREFIX"/bin
+
+# envdir
 cp -v "$SRC_DIR"/envdir "$PREFIX"/bin/envdir
+
+# Nextclade v3
+curl -fsSL -o "$PREFIX"/bin/nextclade3 https://github.com/nextstrain/nextclade/releases/download/3.0.0-alpha.1/nextclade-$("$SRC_DIR"/target-triple)
+chmod a+rx "$PREFIX"/bin/nextclade3
diff --git a/src/target-triple b/src/target-triple
new file mode 100755
index 0000000..15f10e0
--- /dev/null
+++ b/src/target-triple
@@ -0,0 +1,23 @@
+#!/bin/bash
+#
+# Get the target triple from uname.
+#
+set -euo pipefail
+
+kernel="$(uname -s)"
+machine="$(uname -m)"
+
+case "$kernel/$machine" in
+    Linux/x86_64)
+        echo "x86_64-unknown-linux-gnu";;
+
+    Darwin/x86_64)
+        echo "x86_64-apple-darwin";;
+
+    Darwin/arm64)
+        echo "aarch64-apple-darwin";;
+
+    *)
+        echo "unsupported kernel/machine: $kernel/$machine" >&2
+        exit 1;;
+esac

From 9fca5a8480e4f5e04ae6f9d58cef063655b97840 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 22 Dec 2023 12:11:26 -0800
Subject: [PATCH 2/2] Pin Biopython 1.81

Issue linked in changes. Pin to an exact version which is known to be
compatible.
---
 src/recipe.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/recipe.yaml b/src/recipe.yaml
index b54697b..5daf7e2 100644
--- a/src/recipe.yaml
+++ b/src/recipe.yaml
@@ -63,6 +63,8 @@ requirements:
     #
     - awscli
     - bash
+      # Pin Biopython 1.81: https://github.com/nextstrain/augur/issues/1373
+    - biopython =1.81
     - bzip2
     - csvtk
     - curl